dupicc {ENmix} | R Documentation

## Evaluation of measurement reliability using duplicate samples

### Description

The function can be used to evaluate duplicate samples by calculating: 1) centered/un-centered Pearson's correlation coefficient between duplicates; 2) abosolute difference between duplicates; 3) ICC for each CpG probes using oneway or twoway model.

### Usage

    dupicc(dat,dupid,mvalue=FALSE,center=TRUE,nCores=2,qcflag=FALSE,qc=NULL,
           detPthre=0.05,nbthre=3,skipicc=FALSE,corfig=FALSE,model="oneway")

### Arguments

`dat` | Methylation beta value matrix
`dupid` | A data frame with two variables, id1 and id2. The two ids in each row indicate a duplicate pair. These ids should be the same with column names of the input methylation matrix
`mvalue` | If TRUE, the beta value will be converted to M value for calculation of ICC
`center` | If TRUE, the methylation beta values will be centered for each CpG before calculation of ICC or correlation
`nCores` | Number of cores will be used for calculation of ICC
`qcflag` | Whether to perform QC before calculation of ICC
`qc` | QC object from function QCinfo
`detPthre` | If qcflag=TRUE, the methylation values with detection P value higher than the threshold will be removed before calculation
`nbthre` | If qcflag=TRUE, the methylation values with number of bead smaller than the threshold will be removed
`skipicc` | If TRUE, ICC calculation will be skipped
`corfig` | If TRUE, a figure will be generated to demonstrate correlations within duplicates or within non-duplicates
`model` | Using "oneway" or "twoway" model to calculate ICC

### Value

icc: a data frame containing ICC and P values for each probe

dupcor: a data frame containing Pearson's correlation and averaged absolute difference between duplicates.

### Author(s)

Zongli Xu

### References

Zongli Xu, Jack A Taylor. Reliability of DNA methylation measures using Illumina methylation BeadChip. Epigenetics 2020

### Examples

    if (require(minfiData)){
    path <- file.path(find.package("minfiData"),"extdata")
    rgSet <- readidat(path = path,recursive = TRUE)
    mdat=getmeth(rgSet)
    beta=getB(mdat,"Illumina")
    dupidx=data.frame(id1=c("5723646052_R02C02","5723646052_R04C01","5723646052_R05C02"),
    id2=c("5723646053_R04C02","5723646053_R05C02","5723646053_R06C02"))
    iccresu<-dupicc(dat=beta,dupid=dupidx)
    }

[Package ENmix version 1.30.03 Index]